Beyond labels: A review of the application of quantum dots as integrated components of assays, bioprobes, and biosensors utilizing optical transduction

A comprehensive review of the development of assays, bioprobes, and biosensors using quantum dots (QDs) as integrated components is presented. In contrast to a QD that is selectively introduced as a label, an integrated QD is one that is present in a system throughout a bioanalysis, and simultaneously has a role in transduction and as a scaffold for biorecognition. Through a diverse array of coatings and bioconjugation strategies, it is possible to use QDs as a scaffold for biorecognition events. The modulation of QD luminescence provides the opportunity for the transduction of these events via fluorescence resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET), charge transfer quenching, and electrochemiluminescence (ECL). An overview of the basic concepts and principles underlying the use of QDs with each of these transduction methods is provided, along with many examples of their application in biological sensing. The latter include: the detection of small molecules using enzyme-linked methods, or using aptamers as affinity probes; the detection of proteins via immunoassays or aptamers; nucleic acid hybridization assays; and assays for protease or nuclease activity. Strategies for multiplexed detection are highlighted among these examples. Although the majority of developments to date have been in vitro, QD-based methods for ex vivo biological sensing are emerging. Some special attention is given to the development of solid-phase assays, which offer certain advantages over their solution-phase counterparts.     

Synthesis and novel reactivity of halomethyldimethylsulfonium salts

Iodomethyl-, chloromethyl-, and fluoromethyldimethylsulfonium salts, 4b-d, have been synthesized and are observed to be highly reactive molecules that exhibit extraordinary diversity with respect to the nature of their reactivity, undergoing facile direct substitution (S(N)2) reactions, but also being highly susceptible to electron-transfer reactions. Cyclic voltametry experiments indicated that the iodomethyldimethylsulfonium compound, 4b, is a potent electron acceptor, even surpassing the reactivity of perfluoro-n-alkyl iodides in that capacity. The iodo- and chloromethyldimethylsulfonium salts, 4b,c, as well as the analogous iodomethyltrimethylammonium salt, 3a, are shown to be reactive SET acceptors.     

New opportunities in multiplexed optical bioanalyses using quantum dots and donor–acceptor interactions

In this study, we investigated the feasibility of using a novel volatile organic compound (VOC)-based metabolic profiling approach with a newly devised chemometrics methodology which combined rapid multivariate analysis on total ion currents with in-depth peak deconvolution on selected regions to characterise the spoilage progress of pork. We also tested if such approach possessed enough discriminatory information to differentiate natural spoiled pork from pork contaminated with Salmonella typhimurium, a food poisoning pathogen commonly recovered from pork products. Spoilage was monitored in this study over a 72-h period at 0-, 24-, 48- and 72-h time points after the artificial contamination with the salmonellae. At each time point, the VOCs from six individual pork chops were collected for spoiled vs. contaminated meat. Analysis of the VOCs was performed by gas chromatography/mass spectrometry (GC/MS). The data generated by GC/MS analysis were initially subjected to multivariate analysis using principal component analysis (PCA) and multi-block PCA. The loading plots were then used to identify regions in the chromatograms which appeared important to the separation shown in the PCA/multi-block PCA scores plot. Peak deconvolution was then performed only on those regions using a modified hierarchical multivariate curve resolution procedure for curve resolution to generate a concentration profiles matrix C and the corresponding pure spectra matrix S. Following this, the pure mass spectra (S) of the peaks in those region were exported to NIST 02 mass library for chemical identification. A clear separation between the two types of samples was observed from the PCA models, and after deconvolution and univariate analysis using N-way ANOVA, a total of 16 significant metabolites were identified which showed difference between natural spoiled pork and those contaminated with S. typhimurium.     

Characterization of the adsorption of oligonucleotides on mercaptopropionic acid-coated CdSe/ZnS quantum dots using fluorescence resonance energy transfer

Semiconductor quantum dots (QDs) coated with thioalkyl acid ligands are often used as probes and reporters for nucleic acid sensing, or protein sensing using aptamers, and are also potential vectors for gene delivery. In such applications, the interactions that potentially lead to the adsorption of oligonucleotides onto the surface of colloidal QDs are an important consideration. To explore such interactions, fluorescence resonance energy transfer (FRET) between QDs and oligonucleotides labeled with a fluorescent dye was used to identify and characterize a set of conditions that favor strong adsorption on 3-mercaptopropionic acid (MPA)-coated CdSe/ZnS QDs. Adsorption curves and competitive binding experiments were used to determine that the order of affinity for nucleobase adsorption was dC>dA≥dG?dT. The length of the oligonucleotide sequence was also important, with an 80-mer sequence adsorbing more strongly than its 20-mer analog. Adsorption decreased with increasing pH and corresponded to the ionization of the carboxylic acid groups of the MPA ligands. Increased ionic strength partially offsets ligand ionization and increased the extent of adsorption. The interaction between QDs and oligonucleotides was labile, with increases in adsorption at lower concentrations of oligonucleotide and with an increasing number of oligonucleotides per QD. The results were consistent with a hydrogen-bonding model for adsorption, where neutral thioalkyl acid ligands interact favorably with nucleobases and ionized ligands resist adsorption.     

Multidentate surface ligand exchange for the immobilization of CdSe/ZnS quantum dots and surface quantum dot-oligonucleotide conjugates

A method for synthesizing multidentate thiol ligands on fused silica surfaces (e.g., optical fibers) was developed for the immobilization of CdSe/ZnS quantum dots (QDs) capped with hydrophilic or hydrophobic ligands. This work was motivated by the poor stability of QDs immobilized via monodentate thiol ligands and the need for stable immobilization strategies in the development of sensor technologies based on QDs. Multi-dentate immobilization was able to withstand washing protocols, and surface ligand exchange occurred via self-assembly through the zinc-metal affinity interaction. Atomic force and scanning electron microscopy images suggested that the QDs were immobilized at high density, approximately 2-4 x 10 (13) cm (-2). It was possible to immobilize one, two, or three colors of QD. Upon immobilization, 1-2 nm bathochromic shifts in the PL spectra were observed. This was attributed to both ligand exchange and the change in local environment. The change in environment was accompanied by a decrease in PL lifetime. Self-assembly of immobilized QD-oligonucleotide and QD-avidin conjugates was also demonstrated. These conjugates were able to hybridize with complementary oligonucleotide and bind biotin, respectively. This versatile immobilization chemistry is an important step in the development of surface-based QD nanosensors. Such technology requires QDs to be immobilized such that they remain accessible to target molecules in solution.     

Towards multi-colour strategies for the detection of oligonucleotide hybridization using quantum dots as energy donors in fluorescence resonance energy transfer (FRET)

The potential for a simultaneous two-colour diagnostic scheme for nucleic acids operating on the basis of fluorescence resonance energy transfer (FRET) has been demonstrated. Upon ultraviolet excitation, two-colours of CdSe/ZnS quantum dots with conjugated oligonucleotide probes act as energy donors yielding FRET-sensitized acceptor emission upon hybridization with fluorophore (Cy3 and Alexa647) labeled target oligonucleotides. Energy transfer efficiencies, Förster distances, changes in quantum yield and lifetime, and signal-to-noise with respect to non-specific adsorption have been investigated. The dynamic range and limit-of-detection are tunable with the concentration of QD-DNA conjugate. The Cy3 and Alexa647 acceptor schemes can detect target from 4 to 100% or 10 to 100% of the QD-DNA conjugate concentration, respectively. Nanomolar limits of detection have been demonstrated in this paper, however, results indicate that picomolar detection limits can be achieved with standard instrumentation. The use of an intercalating dye (ethidium bromide) as an acceptor to alleviate non-specific adsorption is also described and increases signal-to-noise from S/N < 2 to S/N = 9-10. The ethidium bromide system had a dynamic range from 8 to 100% of the QD-DNA conjugate concentration and could detect target in a matrix containing an excess of non-complementary nucleic acid.     

Fluorescence resonance energy transfer (FRET) for DNA biosensors: FRET pairs and Förster distances for various dye-DNA conjugates

Fluorescence resonance energy transfer (FRET) between the extrinsic dye labels Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethyl Rhodamine (TAMRA), Iowa Black Fluorescence Quencher (IabFQ), and Iowa Black RQ (IabRQ) has been studied. The F?rster distances for these FRET-pairs in single- and double-stranded DNA conjugates have been determined. In particular, it should be noted that the quantum yield of the donors Cy3 and TAMRA varies between single- and double-stranded DNA. While this alters the F?rster distance for a donor-acceptor pair, this also allows for detection of thermal denaturation events with a single non-intercalating fluorophore. The utility of FRET in the development of nucleic acid biosensor technology is illustrated by using TAMRA and IabRQ as a FRET pair in selectivity experiments. The differential quenching of TAMRA fluorescence by IabRQ in solution has been used to discriminate between 0 and 3 base pair mismatches at 60 degrees C for a 19 base sequence. At room temperature, the quenching of TAMRA fluorescence was not an effective indicator of the degree of base pair mismatch. There appears to be a threshold of duplex stability at room temperature which occurs beyond two base pair mismatches and reverses the observed trend in TAMRA fluorescence prior to that degree of mismatch. When this experimental system is transferred to a glass surface through covalent coupling and organosilane chemistry, the observed trend in TAMRA fluorescence at room temperature is similar to that obtained in bulk solution, but without a threshold of duplex stability. In addition to quenching of fluorescence by FRET, it is believed that several other quenching mechanisms are occurring at the surface.     

Adsorption and hybridization of oligonucleotides on mercaptoacetic acid-capped CdSe/ZnS quantum dots and quantum dot-oligonucleotide conjugates

Interest in the unique optical properties of quantum dots (QDs) has resulted in the development QD-bioconjugates for imaging and diagnostics. Although these applications are numerous, considerably less is known about the interactions between QDs and biomolecules. In this work, we describe hydrogen-bonding interactions between oligonucleotides and CdSe/ZnS quantum dots capped with mercaptoacetic acid ligands. The strength of the interactions can be modulated by changes in the pH and ionic strength, the addition of formamide, and differences between ssDNA and dsDNA. Fluorescence resonance energy transfer experiments have shown that conjugated oligonucleotides adopt a conformation that lies across the surface of the QD. The hydrogen-bonding interactions also affect the kinetics of hybridization with QD-DNA conjugates and the thermal stability of QD-conjugated dsDNA. The former is analogous to conventional solid-phase hybridization, where stronger oligonucleotide adsorption leads to faster kinetics. With respect to the latter, interactions with the QD surface can sharpen the melt transition and alter the melt temperature of dsDNA. These effects are largely absent when adsorptive interactions are minimized.